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Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction
Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
* Author to whom correspondence should be addressed.
Received: 3 September 2010; in revised form: 10 September 2010 / Accepted: 15 September 2010 / Published: 29 September 2010
Abstract: Many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features (MoRFs). A well accepted computational tool for identifying likely protein-protein interactions is sequence alignment. In this paper, we propose the combination of sequence alignment and disorder prediction as a tool to improve the confidence of identifying MoRF-based protein-protein interactions. The method of reverse sequence alignment is also rationalized here as a novel approach for finding additional interaction regions, leading to the concept of a retro-MoRF, which has the reversed sequence of an identified MoRF. The set of retro-MoRF binding partners likely overlap the partner-sets of the originally identified MoRFs. The high abundance of MoRF-containing intrinsically disordered proteins in nature suggests the possibility that the number of retro-MoRFs could likewise be very high. This hypothesis provides new grounds for exploring the mysteries of protein-protein interaction networks at the genome level.
Keywords: reverse; retro; invert; alignment; intrinsic disorder; PONDR-RIBS
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Xue, B.; Dunker, A.K.; Uversky, V.N. Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction. Int. J. Mol. Sci. 2010, 11, 3725-3747.
Xue B, Dunker AK, Uversky VN. Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction. International Journal of Molecular Sciences. 2010; 11(10):3725-3747.
Xue, Bin; Dunker, A. Keith; Uversky, Vladimir N. 2010. "Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction." Int. J. Mol. Sci. 11, no. 10: 3725-3747.